SUPV3L1 RNA-Seq in K562

General Information


RBP	SUPV3L1
Cell_Line	K562
Method	shRNA
Exp_Name	SUPV3L1-BGKLV19-K562
ENCODE_series_ID	ENCSR835EXX
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR778SIU
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	SUPV3L1_BGKLV19_53B
Rep2	SUPV3L1_BGKLV19_54B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	79.5
Rep2_qPCR	83.1
Rep1_WB	76.8
Rep2_WB	76.8
Antibody Cat#	A303-056A
Antibody Lot#	A303-056A
Antibody DCC ID	ENCAB067CNB
Status	Released
Project	ENCODE3
ID	483

Experiment Information (Status: Released)

	BGKLV19-53	BGKLV19-54
idx	260	261
TRCN#_or_BGC#	TRCN0000050349	TRCN0000050349
shRNA_or_gRNA_sequence	CCGATACATCAAATGGCCTTT	CCGATACATCAAATGGCCTTT
PAM
Name	SUPV3L1	SUPV3L1
Sample_ID	BGKLV19-53	BGKLV19-54
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	SUPV3L1	SUPV3L1
qPCR_result	79.5	83.1
Ave_qPCR	81.3
RT-qPCR_primer-F	caaatgggaaacaggcttca
RT-qPCR_primer-R	catcctctggctggatctct
protein_conc	2505	2895
WB_result	76.8	76.8
Ave_WB	76.8
WB_DONE_date	1/5/2015
MW	88kDa
IP	1	1
antibody_Cat#	A303-056A	A303-056A
Antibody DCC ID	ENCAB067CNB	ENCAB067CNB
submitted_to_DCC_date	4/2/2015
Rep1_TPM	50.1257404	0
Rep2_TPM	33.770748	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	285	286

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUPV3L1	Product_ID: A303-056A Lot_ID: 1 Source: Bethyl Labs Target Name: SUPV3L1-human

Experiment Status

	BGKLV19-53	BGKLV19-54
Sample_ID	BGKLV19-53	BGKLV19-54
Sample Name	SUPV3L1_BGKLV19_53B	SUPV3L1_BGKLV19_54B
Sample Name	SUPV3L1_BGKLV19_53B	SUPV3L1_BGKLV19_54B
RBP	SUPV3L1	SUPV3L1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	700	701

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-53	BGKLV19-54
Sample #
Sample Name	SUPV3L1-BGKLV19-53B	SUPV3L1-BGKLV19-54B
Sample_Name_Alias	SUPV3L1_BGKLV19_53B	SUPV3L1_BGKLV19_54B
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E11.png	DNA_Library_LV18-19/set1/F11.png
RIN	10.0	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/G1.png	RNA_Library_LV19-21-24/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-53	BGKLV19-54
RBP	SUPV3L1	SUPV3L1
Batch_ID	BGKLV19	BGKLV19
WB_result	76.800	76.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2384	2385

Sequencing Information

	BGKLV19-53	BGKLV19-54
Sample_ID	BGKLV19-53	BGKLV19-54
Sample Name	SUPV3L1_BGKLV19_53B	SUPV3L1_BGKLV19_54B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	43,790,000	42,050,000
total_aligned_reads	40,282,664	38,917,358
unique_aligned_reads	36,350,948	35,465,648
percent_uniqueAligned	0.83012	0.84342
correlation_replicates	0.997887	0.997887
spikein_reads	260,822	241,550
percent_spikeins	0.00596	0.00574
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1026	1027

Data Submission Information

	BGKLV19-53	BGKLV19-53
ENCODE_alias	brenton-graveley:SUPV3L1_BGKLV19	brenton-graveley:SUPV3L1-BGKLV19-K562
ENCODE_accession	ENCSR778SIU	ENCSR835EXX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-53	BGKLV19-53
Sample Name	SUPV3L1_BGKLV19_53B	SUPV3L1_BGKLV19_53B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2898	6997

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
SUPV3L1_BGKLV19_53B_AGTCAA_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1026	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15142
SUPV3L1_BGKLV19_53B_AGTCAA_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1026	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15200
SUPV3L1_BGKLV19_53B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1026					GRCh38	V40	SUPV3L1_BGKLV19_53B_AGTCAA_L006_R1_001.fastq.gz,SUPV3L1_BGKLV19_53B_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	15258
SUPV3L1_BGKLV19_53B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1026					GRCh38	V40	SUPV3L1_BGKLV19_53B/Aligned.sortedByCoord.out.bam		ENCORE2	15329
SUPV3L1_BGKLV19_53B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1026					GRCh38	V40	SUPV3L1_BGKLV19_53B/Aligned.sortedByCoord.out.bam		ENCORE2	15387
SUPV3L1_BGKLV19_53B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1026					GRCh38	V40	SUPV3L1_BGKLV19_53B/Aligned.sortedByCoord.out.bam		ENCORE2	15445
SUPV3L1_BGKLV19_53B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1026					GRCh38	V40	SUPV3L1_BGKLV19_53B/Aligned.sortedByCoord.out.bam		ENCORE2	15503
SUPV3L1_BGKLV19_53B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1026					GRCh38	V40	SUPV3L1_BGKLV19_53B_AGTCAA_L006_R1_001.fastq.gz,SUPV3L1_BGKLV19_53B_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	16400
SUPV3L1_BGKLV19_54B_AGTTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1027	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15143
SUPV3L1_BGKLV19_54B_AGTTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1027	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15201
SUPV3L1_BGKLV19_54B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1027					GRCh38	V40	SUPV3L1_BGKLV19_54B_AGTTCC_L006_R1_001.fastq.gz,SUPV3L1_BGKLV19_54B_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	15259
SUPV3L1_BGKLV19_54B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1027					GRCh38	V40	SUPV3L1_BGKLV19_54B/Aligned.sortedByCoord.out.bam		ENCORE2	15330
SUPV3L1_BGKLV19_54B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1027					GRCh38	V40	SUPV3L1_BGKLV19_54B/Aligned.sortedByCoord.out.bam		ENCORE2	15388
SUPV3L1_BGKLV19_54B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1027					GRCh38	V40	SUPV3L1_BGKLV19_54B/Aligned.sortedByCoord.out.bam		ENCORE2	15446
SUPV3L1_BGKLV19_54B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1027					GRCh38	V40	SUPV3L1_BGKLV19_54B/Aligned.sortedByCoord.out.bam		ENCORE2	15504
SUPV3L1_BGKLV19_54B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1027					GRCh38	V40	SUPV3L1_BGKLV19_54B_AGTTCC_L006_R1_001.fastq.gz,SUPV3L1_BGKLV19_54B_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	16401